You want to split stories and leave sub-tasks behind? Sorry, that's not Agile, so we're not going to make it easy.
You want to Subtask estimates to accrue to the Story estimate? Sorry, that's not Agile, so we're not going to make it easy.
You want to customize the sprint report based on custom labels? Nope, probably not Agile.
You want to plan the capacity of your team to see how much work you should take into an iteration taking into account vacations and partial availability? Sorry, that's not Agile, so we're not going to make it easy.
And on and on, with very basic needs...
I was responsible for bring Jira into my team at 'megabank' not long after it launched around 2003/4, because the alternatives were horrific to set up and use. That was pretty much it.
I've certainly pulled my hair out a million times with Jira, but TBH I'm extremely impressed with their redesign. They've really scaled back the complexity IMO while still giving my team the customizability we need (we started on Trello and quickly hit roadblocks).